Phylogenomic assessment of 23 equid alphaherpesvirus 1 isolates obtained from USA-based equids.

BACKGROUND: Equid alphaherpesvirus 1 (EHV-1) is a global viral pathogen of domestic equids which causes reproductive, respiratory and neurological disease. Few isolates acquired from naturally infected USA-based hosts have been fully sequenced and analyzed to date. An ORF 30 (DNA polymerase) variant (A2254G) has previously been associated with neurological disease in host animals. The purpose of this study was to perform phylogenomic analysis of EHV-1 isolates acquired from USA-based hosts and compare these isolates to previously sequenced global isolates. METHODS: EHV-1 was isolated from 23 naturally infected USA-based equids (6 different states, 15 disease outbreaks) with reproductive (22/23) or neurological disease (1/23). Following virus isolation, EHV-1 DNA was extracted for sequencing using Illumina MiSeq. Following reference-based assembly, whole viral genomes were annotated and assessed. Previously sequenced EHV-1 isolates (n = 114) obtained from global host equids were included in phylogenomic analyses. RESULTS: The overall average genomic distance was 0.0828% (SE 0.004%) for the 23 newly sequenced USA isolates and 0.0705% (SE 0.003%) when all 137 isolates were included. Clade structure was predominantly based on geographic origin. Numerous nucleotide substitutions (mean [range], 179 [114-297] synonymous and 81 [38-120] non-synonymous substitutions per isolate) were identified throughout the genome of the newly sequenced USA isolates. The previously described ORF 30 A2254G substitution (associated with neurological disease) was found in only one isolate obtained from a host with non-neurological clinical signs (reproductive disease), six additional, unique, non-synonymous ORF 30 substitutions were detected in 22/23 USA isolates. Evidence of recombination was present in most (22/23) of the newly sequenced USA isolates. CONCLUSIONS: Overall, the genomes of the 23 newly sequenced EHV-1 isolates obtained from USA-based hosts were broadly similar to global isolates. The previously described ORF 30 A2254G neurological substitution was infrequently detected in the newly sequenced USA isolates, most of which were obtained from host animals with reproductive disease. Recombination was likely to be partially responsible for genomic diversity in the newly sequenced USA isolates.

Calibration of a novel rebound tonometer (Tono-Vera® vet) in the porcine eye.

OBJECTIVE: Porcine models of ocular disease are becoming increasingly utilized. A recently commercialized ocular tonometer, the Reichert Tono-Vera® Vet, has not been evaluated for use in pigs. The purpose of this study was to calibrate this device for use in porcine eyes and to determine which settings are most appropriate for use in pigs. PROCEDURE: The anterior chambers of five freshly enucleated normal porcine eyes were cannulated then connected to a reservoir of balanced salt solution and a physiologic monitor. Triplicate measurements were obtained with the four available settings: dog, cat, horse, and rabbit at intraocular pressures ranging from 5- to 80 mmHg. Bland-Altman analysis was utilized to determine bias and 95% limits of agreement for each setting. RESULTS: There was a strong positive linear regression trend for all settings (dog r2  = 0.986, horse r2  = 0.947, cat r2  = 0.977, and rabbit r2  = 0.982). The linear regression equations for the dog, horse, cat, and rabbit setting were y = 1.0168x - 2.6128, y = 0.8743x - 3.4959, y = 0.9394x - 7.3188, and y = 1.1082x - 3.4077. The average bias and 95% limits of agreement for dog, horse, cat, and rabbit settings were - 2.00, -8.32, -9.58, and 0.57 mmHg, and (-7.52, 3.53), (-19.00, 2.37), (-16.66, -2.50), and (-7.79, 8.93), in mmHg. CONCLUSION: The Tono-Vera® Vet dog setting was most accurate and precise setting compared to true intraocular pressures. This setting is likely to be appropriate for in vivo use in pigs, with the appropriate correction formula applied.

Validation of a novel rebound tonometer (Tono-Vera® Vet) in normal ex vivo rabbit eyes.

OBJECTIVE: The purpose of this study was to validate the use of the Reichert Tono-Vera® Vet tonometer rabbit setting in normal ex vivo rabbit eyes and to compare the rabbit setting to the dog, cat, and horse settings of this tonometer. PROCEDURE: Six freshly enucleated normal rabbit eyes were cannulated and connected to a fluid reservoir and physiologic monitor. Triplicate measurements were obtained with the four available settings: dog, cat, horse, and rabbit at various intraocular pressures (IOP) ranging from 5 to 80 mmHg. Bland-Altman analysis was utilized to determine bias and 95% limits of agreement for each setting. RESULTS: Linear regression equations for the dog, horse, cat, and rabbit settings were y = 0.8101x + 2.5058, y = 0.7594x - 3.4673, y = 0.6635x + 0.3021, and y = 0.8935x + 1.3295, respectively. All settings demonstrated strong positive linear trends (dog r2 = 0.9644, horse r2 = 0.9456, cat r2 = 0.9309, and rabbit r2 = 0.9558). Bland-Altman plots revealed that the average bias and 95% limits of agreement (mmHg) were -4.73, -12.65, -12.86 and -2.73 and (-15.31, 5.86), (-29.03, 3.74), (-25.67, -0.05), and (-12.21, 6.76) for the dog, horse, cat, and rabbit settings, respectively. CONCLUSION: The Tono-Vera® Vet rabbit setting provided the most accurate and precise measurements compared with the other settings, but slightly underestimated actual IOP, especially as IOP was increased. This tonometer, using the rabbit setting, is likely to be appropriate for the estimation of IOP in rabbits with the appropriate correction formula applied.

Relationship between the bacterial ocular surface microbiota and outcomes for cats with feline herpesvirus type 1 ocular surface disease.

OBJECTIVE: Feline herpesvirus 1 (FHV-1) causes ocular surface disease in domestic cats. The purpose of this study was to assess the relationship between bacterial ocular surface microbiota and outcomes for cats with FHV-1 ocular surface disease. ANIMALS STUDIED: Twenty-two shelter-housed cats with confirmed FHV-1 ocular surface disease. PROCEDURES: Animals were grouped according to FHV-1 shedding and ocular clinical scores following intervention: worsened outcome (WorOut, n = 11) or improved outcome (ImpOut, n = 11). Scoring and conjunctival sampling were completed on Days 1 and 8 of twice daily antiviral treatment. Bacterial DNA was extracted and submitted for 16S rRNA gene sequencing. Real-time polymerase chain reaction was performed for selected bacterial species. Overall DNA concentration between groups was assessed. RESULTS: Bacterial microbiota relative abundance composition was significantly different between ImpOut and WorOut groups (weighted UniFrac p = .006). Alpha diversity was significantly higher in the ImpOut group compared with the WorOut group (Shannon p = .042, Simpson's p = .022, Pielou's p = .037). Differences in the relative abundance of various phyla and species were detected between groups. Total DNA concentration was higher in the WorOut group compared with the ImpOut group (p = .04). Feline GAPDH (p = .001) and Bilophila wadsworthia (p = .024) copy number was significantly higher in the ImpOut group compared with the WorOut group. CONCLUSIONS: The results highlight the important relationship between the bacterial ocular surface microbiota and FHV-1 infection outcomes in cats treated with antiviral medications. Low bacterial species diversity, higher overall DNA (presumed predominantly bacterial) load, and certain bacterial phyla/species were associated with poor outcomes for cats with FHV-1 ocular disease.

Surveillance for feline herpesvirus type 1 mutation and development of resistance in cats treated with antiviral medications.

Feline herpesvirus type 1 (FHV-1) commonly causes ocular surface disease in cats and is treated with antiviral medications targeting viral DNA polymerase (UL30/42). Herein, we describe a method to assess the FHV-1 genome for mutation development and to assess the functional impact of mutations, if present. Fourteen shelter-housed domestic cats with FHV-1 ocular surface disease were assigned to one of four treatment groups: placebo (n = 3), cidofovir 0.5% ophthalmic solution (n = 3), famciclovir oral solution (n = 5), or ganciclovir 0.15% ophthalmic solution (n = 3). Swabs were collected before (day 1) and after (day 8) 1 week of twice-daily treatments to isolate viable FHV-1. Viral DNA was extracted for sequencing using Illumina MiSeq with subsequent genomic variant detection between paired day 1 and day 8 isolates. Plaque reduction assay was performed on paired isolates demonstrating non-synonymous variants. A total of 171 synonymous and 3 non-synonymous variants were identified in day 8 isolates. No variants were detected in viral UL23, UL30, or UL42 genes. Variant totals were not statistically different in animals receiving antiviral or placebo (p = 0.4997). A day 8 isolate from each antiviral treatment group contained a single non-synonymous variant in ICP4 (transcriptional regulator). These 3 isolates demonstrated no evidence of functional antiviral resistance when IC50 was assessed. Most (10/14 pairs) day 1 and 8 viral isolate pairs from the same host animal were near-identical. While functional variants were not detected in this small sample, these techniques can be replicated to assess FHV-1 isolates suspected of having developed resistance to antiviral medications.